Creative Release gives us Etoile, who is a very explicit expy of Ikari Shinji (he's a pilot who protects his planet from alien attacks and has doubts about his motivations).
Natasha Wing from Electric Wonderland became introduced after Peter Paltridge's disgust with Chuck character Anna Wu playing a progressively smaller role compelled him to make his own Asian Action Girl.
Bro's rapping vetriloquist dummy Lil' Cal in Homestuck shares a large number of traits with Franklin from Arrested Development, one of Hussie's favourite shows.
In Act 6, we meet the Alpha kids, aka alternate universe counterparts of the original kid's guardians, who share some similarities to the dead trolls. Jane Crocker shares many similarities to Feferi and is related to her by adoption, Jake English has similarities to Equius and mirrors Eridan in many ways, Roxy is an odd mix of Sollux, Gamzee, and Nepeta, and Dirk is Equius and Rose.
Lindesfarne from Kevin & Kell fulfills a very similar role to that of Samantha from Safe Havens: a kind, witty and intelligent scientist. Both were created by Bill Holbrook.
The Law of Purple has several characters who are explicitly expies of Yu-Gi-Oh! characters: Lette, who is Seto Kaiba with boobs and a sense of humor, Juni, who is based on Alister, and Carli/y/eigh, who is Zigfried von Schroeder.
In-universe case in MegaTokyo. Kotone, the Ill Girl Kimiko is voicing in a game, is an expy of Tohya Miho, just like all other in-universe Ill Girls. Miho's story touched the world so much that it became more real than she ever was. One of the side effects of this is that she created the Ill Girl trope as writers tried to capture the emotion of her story. The other is that it brought her back to life to relive her sickness and die again. And again and again and again...
The characters of Mike Bookseller all work at a stand in for Barnes & Noble called Booksellers. Another bookstore (standing in for the now extinct Borders chain) appeared in the comic by the name of Booktraders.
Survivor: Fan Characters, being based on the reality TV show, sometimes bases its characters on real-life Survivor contestants. Some of the most obvious examples are Season 3's Baxter having a dynamic patterned after the "Manipulative Bastard angers the jury too much to win" one like Boston Rob from All-Stars, and Season 7's Ventious having the leadership and charisma of Tom of Palau or J.T. from Tocantins (but not the Flawless Victory) and Ker from the same season being a lovable eccentric who ended up immunitying her way to the win much like Fabio's in Nicaragua.
Olivia, Tate, and Zoey from Weesh are rather obviously modeled on Alex, Riley, and Tristan from the author's earlier Angel Moxie. (Zoey is a teenager and Tate is a boy, but other than that...)